Dear Consortium Members and Affiliates,
As we scramble to put things back in order after the Thanksgiving break, we've got a few nuggets of goodness to share in our monthly SBGrid update. Read on for our latest webinar news, an introduction to SBGrid member Ramaswamy Subramanian, a reminder to deposit your X-ray diffraction datasets when submitting your manuscripts for review, a software push with 10 updates and 2 new titles, 2 new members to welcome, and 3 publication highlights.
We had a great turnout earlier this month for our webinar featuring Sjors Scheres and RELION 3.0. If you missed the live presentation, you can catch up with the recorded version on YouTube. We'll squeeze in a December webinar next week, before the holiday season swallows up free time, so don't forget to join us Dec 4th to hear from Nick Pearce on PanDDA: extracting ligand-bound protein states from conventionally uninterpretable crystallographic electron density.
We made our way to India, for our November member tale, to hear from Ramaswamy Subramanian (aka Rams) at the Institute for Stem Cell Biology and Regenerative Medicine. Rams lets curiosity act as a key driver for research projects in his laboratory, helping to launch investigations into why North American walleye fish turn blue and how a mother cockroach's milk crystals nourish embryos. Read the full story.
Ready to submit a manuscript and wondering how to keep track of those X-ray diffraction datasets so you can easily reprocess data for revisions? Check out the SBGrid Data Bank, a repository storing close to 500 public datasets from 80 different laboratories. Dozens of additional datasets are on-hold, awaiting author approval after publication of the final manuscript. Deposit your data here.
Our November software update includes new versions of CCP4, Chimera, ChimeraX, crYOLO, DIALS, MotionCor2, PyMOL, Rosetta, STAMP, THUNDER, and two new applications: BioPython and goCTF.
Four new members joined SBGrid in the month of November, David Haselbach and Clemens Plaschka from IMP Vienna, Yongna Xing from the University of Wisconsin, and Melanie Ott of the Gladstone Institute UCSF. Welcome to our newest members!
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the SBGrid Data Bank along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
Seven new citations appeared for SBGrid's eLife paper in November, with acknowledgements appearing in an eLife paper from Susan Shao's Harvard Medical School laboratory [Abstract], a publication in PNAS from Caltech's Douglas Rees [Abstract], Jean-Philippe Julien's, Nature Communications article from SickKids, University of Toronto [Abstract], a Journal of Biological Chemistry paper from SBGrid members Jay Nix at Lawrence Berkley National Labs and Tom Brett of Washington University [Abstract], an article from Alexandre Bonvin's University Utrecht group in Journal of Molecular Biology [Abstract], and a publication from SBGrid members Navtej Toor and K. Rajashankar from UC San Diego and Lawrence Berkley National Labs in Nature Communications.
Over 20 member publications appeared in journals this month. You can find a complete listing on our website, along with a few notable highlights below:
- Andrei Yudin of the University of Toronto has a new publication in Drug Discovery Today: Technologies, discussing the current protocols for the preparation of boron-containing molecules (BCMs) from multicomponent reactions with borylated building blocks. With the discovery of the anti-cancer drug bortezomib, which is an organoboron reagent, finding easier methods for the preparation of BCMs has wide therapeutic potential in the fight against cancer. [Abstract]
- Ramaswamy Subramanian of the Institute for Stem Cell Biology and Regenerative Medicine, NCBS, India, has a new paper in Acta Crystallographica, where his group solved the structures of N-Acetyl-D-neuraminic acid lyase from Fusobacterium nucleatum (FnNanA) in the ligand-free and ligand-bound states. Since FnNanA is implicated in gingivitis and periodontal diseases, this discovery could lead to new targets for the treatment of gum disease. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a new paper that appeared in Nature Communications from Patrick Hogan's group at La Jolla Institute for Allergy & Immunology in which they describe new calcium binding sites in STIM1 that interact with the previously known EF-hand site to revise our understanding of STIM1 calcium sensing. More on Tumblr.
BioPython version 1.72 is new to SBGrid. BioPython is a set of tools for biological computation written in Python in a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
CCP4 is now at version 7.0.066. This version includes a fix in pointless for ambiguous Laue group results; a fix to arcimboldo output for P1 space group and for BORGES; restraints added for LIBG for DNA/RNA in lorestr; a database update in morda; updates to rabdam, fragon, ccp4i2, and crank2; and bug fixes to nautilus pipeline, sequence import, and crank2.
Chimera version 1.13 includes an updated CASTp fetch URL, a new serial-numbering option for saving very large PDB files, changes to the swapaa, tile, and write commands, and a fix to the Modeller input preparation.
ChimeraX was updated to version 0.7, with the 0.8.daily build available via version override. See the change log for full details.
crYOLO 1.1.4-cpu was pushed out.
DIALS is now at version 11.4
goCTF is also new to SBGrid. goCTF is used for geometrically-optimized CTF determination for single-particle cryo-EM.
MotionCor2 1.2.1 was pushed out.
PyMOL was updated to version 2.2.3.
Rosetta 3.10 is the new default.
THUNDER is now at version 1.4.11, which was bumped a few versions after ironing out licensing issues. In 1.4 THUNDER was upgraded to allow it to run on GPU clusters, and since then the developers have improved the stability of 2D classification, added support for NVIDIA V100, included a new graphical user interface - thunder_stackview - for viewing the result of 2D classification and selecting desired particles, and cleaned up a few bugs.
STAMP version 4.4.1 is the new default. With this update STAMP is now licensed under the GNU General Public License. The developers have also updated manual to reflect minor changes in the output format, modified source code for Mac OS X compiling, and updated the bundled SCOP domain databases to SCOP release 1.75.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.